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- PDB-1yh3: Crystal structure of human CD38 extracellular domain -

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Basic information

Entry
Database: PDB / ID: 1yh3
TitleCrystal structure of human CD38 extracellular domain
ComponentsADP-ribosyl cyclase 1
KeywordsHYDROLASE / parallel beta sheets / two domains / membrane association / cell surface receptor
Function / homology
Function and homology information


2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / artery smooth muscle contraction / Nicotinate metabolism / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / negative regulation of bone resorption / response to hydroperoxide ...2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / artery smooth muscle contraction / Nicotinate metabolism / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / negative regulation of bone resorption / response to hydroperoxide / long-term synaptic depression / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / B cell proliferation / response to retinoic acid / positive regulation of B cell proliferation / positive regulation of vasoconstriction / response to interleukin-1 / response to progesterone / female pregnancy / apoptotic signaling pathway / B cell receptor signaling pathway / positive regulation of insulin secretion / negative regulation of neuron projection development / response to estradiol / positive regulation of cytosolic calcium ion concentration / transferase activity / positive regulation of cell growth / basolateral plasma membrane / nuclear membrane / response to hypoxia / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
ADP Ribosyl Cyclase; Chain A, domain 1 / ADP Ribosyl Cyclase; Chain A, domain 1 / ADP-ribosyl cyclase (CD38/157) / ADP-ribosyl cyclase / NAD(P)-binding Rossmann-like Domain / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsLiu, Q. / Kriksunov, I.A. / Graeff, R. / Munshi, C. / Lee, H.C. / Hao, Q.
CitationJournal: Structure / Year: 2005
Title: Crystal structure of human CD38 extracellular domain.
Authors: Liu, Q. / Kriksunov, I.A. / Graeff, R. / Munshi, C. / Lee, H.C. / Hao, Q.
History
DepositionJan 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 20, 2021Group: Advisory / Database references
Category: database_2 / pdbx_database_remark / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _struct_ref_seq_dif.details
Remark 999SEQUENCE Prasad G.S., McRee D.E., Stura E.A., Levitt D.G., Lee H.C., Stout C.D. "Crystal structure ...SEQUENCE Prasad G.S., McRee D.E., Stura E.A., Levitt D.G., Lee H.C., Stout C.D. "Crystal structure of Aplysia ADP ribosyl cyclase, a homologue of the bifunctional ectozyme CD38." Nat Struct Biol. 1996 Nov;3(11):957-64 Jackson D.G., Bell J.I. "Isolation of a cDNA encoding the human CD38 (T10) molecule, a cell surface glycoprotein with an unusual discontinuous pattern of expression during lymphocyte differentiation." J. Immunol. 144:2811-2815(1990)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-ribosyl cyclase 1
B: ADP-ribosyl cyclase 1


Theoretical massNumber of molelcules
Total (without water)59,2992
Polymers59,2992
Non-polymers00
Water5,837324
1
A: ADP-ribosyl cyclase 1


Theoretical massNumber of molelcules
Total (without water)29,6501
Polymers29,6501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosyl cyclase 1


Theoretical massNumber of molelcules
Total (without water)29,6501
Polymers29,6501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.839, 51.491, 66.439
Angle α, β, γ (deg.)108.27, 90.47, 97.29
Int Tables number1
Space group name H-MP1
DetailsThe active assembly is a monomer

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Components

#1: Protein ADP-ribosyl cyclase 1 / Cyclic ADP-ribose hydrolase 1 / cADPr hydrolase 1 / Lymphocyte differentiation antigen CD38 / T10 / ...Cyclic ADP-ribose hydrolase 1 / cADPr hydrolase 1 / Lymphocyte differentiation antigen CD38 / T10 / Acute lymphoblastic leukemia cells antigen CD38


Mass: 29649.637 Da / Num. of mol.: 2 / Fragment: human CD38 extracellular domain / Mutation: N100D, N164A, N219D, N209D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P28907, NAD+ glycohydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES, PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.916 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2004
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 41065 / Num. obs: 40203 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.9→1.93 Å / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→10 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.383 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25336 1992 5.1 %RANDOM
Rwork0.18849 ---
all0.19174 39418 --
obs0.19174 37426 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.562 Å2
Baniso -1Baniso -2Baniso -3
1--2.17 Å20.66 Å21.21 Å2
2--1.15 Å22.56 Å2
3---2.81 Å2
Refinement stepCycle: LAST / Resolution: 1.91→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3986 0 0 324 4310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0214102
X-RAY DIFFRACTIONr_angle_refined_deg2.2641.9335556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3345502
X-RAY DIFFRACTIONr_chiral_restr0.1740.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023117
X-RAY DIFFRACTIONr_nbd_refined0.2630.21990
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4090.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.223
X-RAY DIFFRACTIONr_mcbond_it1.5391.52496
X-RAY DIFFRACTIONr_mcangle_it2.65924035
X-RAY DIFFRACTIONr_scbond_it4.231606
X-RAY DIFFRACTIONr_scangle_it6.2974.51521
LS refinement shellResolution: 1.91→1.958 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.296 154
Rwork0.254 2617
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.7149-1.13220.06060.9474-0.59250.2239-0.0504-0.3318-0.27040.12920.04570.1163-0.01880.01780.00460.274-0.0364-0.04160.23730.02330.30276.5239-16.9153.2326
20.9815-0.6602-0.06161.09950.05470.07280.0498-0.0038-0.1528-0.0035-0.01380.08170.022-0.0323-0.03590.2916-0.0147-0.01640.2397-0.03770.2743-0.3784-6.6536-4.0478
31.0015-0.63530.11141.2881-0.0131-0.17360.05710.0267-0.1240.0163-0.0295-0.0671-0.0511-0.0362-0.02760.293-0.0113-0.01270.2534-0.0210.27788.5322-4.6144-2.735
41.05440.1020.23380.56930.42061.51870.03070.0460.12840.0557-0.0073-0.09880.03290.0915-0.02340.2992-0.0152-0.00290.2442-0.02270.25741.712311.6322-1.2744
51.4284-0.25540.20311.4653-0.56411.31910.0534-0.1560.40410.13130.0448-0.0448-0.20180.0356-0.09820.2846-0.0213-0.00660.2355-0.07210.2356-2.803316.842.8088
62.9104-0.93710.5118-0.6006-2.05233.2073-0.0372-0.07220.40590.10160.1495-0.0422-0.0847-0.0412-0.11230.2984-0.01330.03180.216-0.03380.3099-16.620413.6166-7.9169
75.3329-0.31590.62680.43511.84292.24430.09350.95241.03040.03140.0533-0.4557-0.60210.1799-0.14690.30150.01110.18970.36590.36580.4717-16.066226.165-30.6222
80.9389-0.0257-2.16810.39270.80184.11940.26920.2970.54280.0011-0.1987-0.1247-0.0622-0.5186-0.07060.23290.07570.04280.30680.10850.3611-29.054620.3772-18.4534
90.2979-0.3072-0.10733.78640.28541.45170.19840.36470.0437-0.1717-0.0128-0.1189-0.0902-0.1489-0.18560.24370.13110.0670.58420.17520.1112-19.408310.3727-38.2651
101.9645-0.3624-0.64320.08260.87231.37540.14450.31220.30960.0714-0.054-0.11880.0165-0.1807-0.09050.24310.00390.02470.30520.0560.2724-22.486213.7872-19.4379
111.3353-0.098-0.40322.39340.8051.28540.14130.0207-0.0469-0.1747-0.28380.0530.0759-0.04530.14260.26130.0983-0.00570.45420.05840.087-24.8185-1.6246-39.5095
129.6033-2.7376-5.3451-2.6287-0.818520.55920.72660.5329-0.01130.010.11520.0202-0.2218-1.3543-0.84180.1952-0.0694-0.0520.26010.02530.3783-13.5005-11.9796-8.9371
13-0.004611.5103-12.081924.12828.03615.8059-0.09650.08730.1657-0.17530.12181.6573-0.9721-0.4276-0.02520.28550.01390.00740.2836-0.0080.2851-20.8978.946912.0801
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 72
2X-RAY DIFFRACTION2A81 - 160
3X-RAY DIFFRACTION3A161 - 210
4X-RAY DIFFRACTION4A211 - 244
5X-RAY DIFFRACTION5A256 - 286
6X-RAY DIFFRACTION6B45 - 60
7X-RAY DIFFRACTION7B61 - 88
8X-RAY DIFFRACTION8B89 - 110
9X-RAY DIFFRACTION9B111 - 142
10X-RAY DIFFRACTION10B143 - 192
11X-RAY DIFFRACTION11B193 - 296
12X-RAY DIFFRACTION12A73 - 80
13X-RAY DIFFRACTION13A287 - 296

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